Update file ancient_MRSA_assignment.md

assignments/ancient_MRSA_assignment.md

@@ -6,7 +6,7 @@ Please download the raw data (illumina and nanopore reads) into your own data sp
 cp -r /shares/amr.imm.uzh/data/projects/Blockcourse_BIO296/FS2023/Participants_data/ancient_MRSA [target_directory]
 ```
 
-
+## Scripts
 You can find all scripts we have used previously for the MRSA/UPEC exercises in the following locations. 
 PLEASE COPY ANY SCRIPT YOU MIGHT NEED TO YOUR OWN DATA SPACE BEFORE EDITING. 
 
@@ -22,3 +22,36 @@ PLEASE COPY ANY SCRIPT YOU MIGHT NEED TO YOUR OWN DATA SPACE BEFORE EDITING.
 /shares/amr.imm.uzh/data/projects/Blockcourse_BIO296/FS2023/Participants_data/nanopore_scripts
 ```
 
+## Software
+
+If you want to have a look at the manuals for the different software we use:
+
+**QC & Assembly**
+
+FastQC: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
+
+Trimmomatic: http://www.usadellab.org/cms/?page=trimmomatic
+
+Unicycler: https://github.com/rrwick/Unicycler
+
+BWA: https://github.com/lh3/bwa
+
+Samtools: https://www.htslib.org
+
+Pilon: https://github.com/broadinstitute/pilon
+
+Quast: https://github.com/ablab/quast
+
+
+**Annotation**
+Prokka: https://github.com/tseemann/prokka
+
+
+**Variant calling & phylo**
+
+Snippy: https://github.com/tseemann/snippy
+
+Seqtk: https://github.com/lh3/seqtk
+
+IQ-Tree: http://www.iqtree.org
+